I just ran into this strange situation on Portal 10.5. I was unable to find a BUG in the support site that described the issue and the list of resolved issues in 10.5.1 did not appear to contain it, either.
I wanted to create an Application Item in Portal that points to an application in my ArcGIS Online Organizational account using a URL like http://myorg.maps.arcgis.com/apps/webappviewer/index.html?id=1fe52f64640247c99c772de938809f7a
Once I click the Add Item, the item is created, but the URL is not pointing at the Portal URL with the ArcGIS Online Item ID appended
If I look at the item's JSON data in AGO Assistant, the correct URL is present. So it appears to be a bug in the Home application where the URL is being interpreted and transformed into an local Portal URL.
I was able to work around the issue by using a URL shortening service on my original URL and saving the shortened URL in the Portal Application Item, but I would like to either find a way to prevent the Home application from transforming my URL, or know if this is a BUG that is fixed in Portal 10.5.1.